>My questions are: Am I doing right so far?
I would have stopped feeding when they got a little stocked up and there was a nectar flow, but it seems to be working.
> Is it necessary to use the smoker?
I would light it. You many not need it, but you disrupt them more with them getting into a major defensive than from smoking them.
> I have not used it once, and have inspected the hive and filled the feeder every 4 days so far.
But one day they will will rebel.
It doesn't take but one puff across the top bars to make a world of difference on a day they are in a bad mood.
> Can or should I have more than 2 boxes for brood?
I think so. Some people don't. But then you're running deeps and if they fill it full of honey it will weigh 90 pounds.
> Some of the drawn wax is yellow, and some is pure white. Any one know why this is?
It's normal. They track pollen on the wax and it gets yellow. Over time it gets brown then eventually black. Cocoons (from brood) will speed the process of getting to black.
> Before I put the second box on, they were building comb on top of the frames, and on the bottom of the inner cover. I scraped it off, and they have continued in the same place on the second box, even though the frames are not all drawn out yet.
I wouldn't worry too much about it. But maybe you have the inner cover on upside down. The space bewteen the top bars and the lid should be between 1/4" and 3/8".
> There is also quite a variance in the appearance of the workers. Some are nearly black, and some are smaller, and some are very light in color. Is this normal, and why is it?
The queen is open mated. She may have mated with many different drones and may have offspring with many different characteristics. That and, as mentioned above, they package bees with whatever is around, not with that queens offspring.